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Old 11-06-2013, 01:55 PM   #1
jor12345
Junior Member
 
Location: Cologne, Germany

Join Date: Nov 2013
Posts: 3
Default HPC cluster : make error : make[2]: *** [bundles.o] Error 1

Hi all!

I am having a problem installing cufflinks on a HPC cluster.

Here is what happens before the error comes up when doing make

Code:
bundles.cpp:680:23: Warnung: Ganzzahlkonstante ist so gross, dass sie vorzeichenlos ist
bundles.cpp:680: Warnung: diese Dezimalkonstante ist nur in ISO-C90 vorzeichenlos
bundles.cpp:680: Fehler: Ganzzahlkonstante ist zu gross f?r >>long<<-Typ
progressbar.h: In constructor >>ProgressBar::ProgressBar(std::string, double)<<:
progressbar.h:28: Warnung: Umwandlung in >>int<< von >>double<<
progressbar.h: In member function >>void ProgressBar::update(const char*, double)<<:
progressbar.h:61: Warnung: Umwandlung in >>int<< von >>long double<<
progressbar.h: In member function >>void ProgressBar::remaining(int)<<:
progressbar.h:81: Warnung: Umwandlung in >>int<< von >>long double<<
bundles.cpp: In member function >>bool HitBundle::add_open_hit(boost::shared_ptr<const ReadGroupProperties>, const ReadHit*, bool)<<:
bundles.cpp:296: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
bundles.cpp:305: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
bundles.cpp: In member function >>void HitBundle::finalize(bool)<<:
bundles.cpp:563: Warnung: Umwandlung in >>size_t<< von >>float<<
bundles.cpp: In member function >>bool BundleFactory::next_bundle_hit_driven(HitBundle&)<<:
bundles.cpp:796: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
bundles.cpp: In member function >>bool BundleFactory::next_bundle_ref_driven(HitBundle&)<<:
bundles.cpp:838: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
bundles.cpp:878: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
/scratch/martinsj/RNAseq/include/boost/system/error_code.hpp: At global scope:
/scratch/martinsj/RNAseq/include/boost/system/error_code.hpp:222: Warnung: >>boost::system::posix_category<< definiert, aber nicht verwendet
/scratch/martinsj/RNAseq/include/boost/system/error_code.hpp:223: Warnung: >>boost::system::errno_ecat<< definiert, aber nicht verwendet
/scratch/martinsj/RNAseq/include/boost/system/error_code.hpp:224: Warnung: >>boost::system::native_ecat<< definiert, aber nicht verwendet
make[2]: *** [bundles.o] Error 1
make[2]: Leaving directory `/scratch/martinsj/RNAseq/cufflinks-2.1.1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/scratch/martinsj/RNAseq/cufflinks-2.1.1'
make: *** [all] Error 2
here is the command line before doing make:

Code:
./configure --prefix=$scr/martinsj/RNAseq --with-boost=$scr/martinsj/RNAseq --with-eigen=$scr/martinsj/RNAseq/include --with-bam=$scr/martinsj/RNAseq
and the resulting output

Code:
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking for gawk... (cached) gawk
checking for g++... g++
checking for C++ compiler default output file name... a.out
checking whether the C++ compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ANSI C... none needed
checking dependency style of gcc... gcc3
checking whether make sets $(MAKE)... (cached) yes
checking for ranlib... ranlib
checking for a BSD-compatible install... /usr/bin/install -c
checking for a Python interpreter with version >= 2.4... python
checking for python... /usr/bin/python
checking for python version... 2.4
checking for python platform... linux2
checking for python script directory... ${prefix}/lib/python2.4/site-packages
checking for python extension module directory... ${exec_prefix}/lib/python2.4/site-packages
checking for boostlib >= 1.47.0... yes
checking for bamlib... yes
checking build system type... i686-pc-linux-gnu
checking whether the Boost::System library is available... yes
checking for exit in -lboost_system... yes
checking for exit in -lboost_system... (cached) yes
checking whether the Boost::Thread library is available... yes
checking for exit in -lboost_thread... yes
checking for exit in -lboost_system... (cached) yes
checking how to run the C preprocessor... gcc -E
checking for egrep... grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking if zlib is wanted... yes
checking for inflateEnd in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for inflateEnd in -lz... (cached) yes
checking zlib in /usr... ok
checking for eigenlib... checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for pid_t... yes
checking for size_t... yes
checking for ptrdiff_t... yes
checking host system type... i686-pc-linux-gnu
checking for struct sysinfo.totalram... yes
checking whether sysctl is declared... yes
checking whether CTL_HW is declared... no
checking whether HW_PHYSMEM is declared... no
checking how to create a pax tar archive... gnutar
checking dependency style of gcc... (cached) gcc3
checking dependency style of g++... (cached) gcc3
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands


-- cufflinks 2.1.1 Configuration Results --
  C++ compiler:        g++ -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -march=i686 -O3  -DNDEBUG  -pthread -I/scratch/martinsj/RNAseq/include -I/scratch/martinsj/RNAseq/include -I/scratch/martinsj/RNAseq/include/include  
  GCC version:         gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-54)
  Host System type:    i686-pc-linux-gnu
  Install prefix:      /scratch/martinsj/RNAseq
  Install eprefix:     ${prefix}


  See config.h for further configuration information.
  Email <cole@cs.umd.edu> with questions and bug reports.
Boost is properly installed as it could be detected and works properly for tophat. I've also tried to use a different boost version 1.47 but the outcome was the same.

I've added the

Code:
#ifndef BOOST_SYSTEM_NO_DEPRECATED
#define BOOST_SYSTEM_NO_DEPRECATED 1
#endif
to the head of my bundles.cpp file in src but now I get the following error

Code:
bundles.cpp:684:23: Warnung: Ganzzahlkonstante ist so gross, dass sie vorzeichenlos ist
bundles.cpp:684: Warnung: diese Dezimalkonstante ist nur in ISO-C90 vorzeichenlos
bundles.cpp:684: Fehler: Ganzzahlkonstante ist zu gross f?r >>long<<-Typ
progressbar.h: In constructor >>ProgressBar::ProgressBar(std::string, double)<<:
progressbar.h:28: Warnung: Umwandlung in >>int<< von >>double<<
progressbar.h: In member function >>void ProgressBar::update(const char*, double)<<:
progressbar.h:61: Warnung: Umwandlung in >>int<< von >>long double<<
progressbar.h: In member function >>void ProgressBar::remaining(int)<<:
progressbar.h:81: Warnung: Umwandlung in >>int<< von >>long double<<
bundles.cpp: In member function >>bool HitBundle::add_open_hit(boost::shared_ptr<const ReadGroupProperties>, const ReadHit*, bool)<<:
bundles.cpp:300: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
bundles.cpp:309: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
bundles.cpp: In member function >>void HitBundle::finalize(bool)<<:
bundles.cpp:567: Warnung: Umwandlung in >>size_t<< von >>float<<
bundles.cpp: In member function >>bool BundleFactory::next_bundle_hit_driven(HitBundle&)<<:
bundles.cpp:800: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
bundles.cpp: In member function >>bool BundleFactory::next_bundle_ref_driven(HitBundle&)<<:
bundles.cpp:842: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
bundles.cpp:882: Warnung: Vergleich zwischen vorzeichenbehafteten und vorzeichenlosen Ganzzahlausdr?cken
make[2]: *** [bundles.o] Error 1
make[2]: Leaving directory `/scratch/martinsj/RNAseq/cufflinks-2.1.1/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/scratch/martinsj/RNAseq/cufflinks-2.1.1'
make: *** [all] Error 2
Can anyone help?

Best!
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Old 11-06-2013, 03:50 PM   #2
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,814
Default

Are you able to use the binary? That could solve this problem. http://cufflinks.cbcb.umd.edu/downlo..._x86_64.tar.gz

If not what cluster OS are you trying to compile on? Have you tried to use the newest boost lib?
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Old 11-06-2013, 11:46 PM   #3
jor12345
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Location: Cologne, Germany

Join Date: Nov 2013
Posts: 3
Default

Can't use the binary

Code:
$ cufflinks ./test_data.sam
-bash: /scratch/martinsj/RNAseq/bin/cufflinks: cannot execute binary file
I've tried boost 1.54, 1.55 beta, and 1.47, error was always the same.


>>Cluster<<

Operating system: Linux
Number of nodes: 841
Number of cores: 9712
Memory: 35,5 TB

The node interconnect is based on InfiniBand QDR. INCA compute nodes providing two Intel Nehalem EP quad-core processors (Xeon X5550) and Intel Westmere hexa-core processors (Xeon X5650), respectively. MESCA nodes equipped with four Intel Nehalem EX octo-core processors (Xeon X7560).

Thanks!!
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Old 11-07-2013, 02:09 AM   #4
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479
Default

This is probably due to the use of an ancient version of gcc (4.1.2 is 6.5 years old!).

The compilation is aborting due to
Code:
Fehler: Ganzzahlkonstante ist zu gross für >>long<<-Typ
or 'Error, integer constant is too large for type "long"' for us Ausländer. The cause of this is pretty apparent if you look at bundles.cpp:
Code:
if (tmp.ref_id() == 12638153115695167477)  // corresponds to SAM "*" under FNV hash. unaligned read record
You might be able to make the following change and get things to work:
Code:
if (tmp.ref_id() == 12638153115695167477ULL)  // corresponds to SAM "*" under FNV hash. unaligned read record
but I don't actually know if that version of g++ can handle that (a bit of googling suggests that this wasn't even in the C++ standard when that version of g++ was released!). If making that change works, then great. Otherwise, you'll probably just need to use a more recent version of gcc.
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Old 11-07-2013, 04:09 AM   #5
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,814
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I will confirm Devon's assessment. You should try to upgrade the GCC (to the newest version if possible) otherwise even if you are able to get it to compile it will cause seg faults once you start running.
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Old 11-08-2013, 12:02 PM   #6
jor12345
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Location: Cologne, Germany

Join Date: Nov 2013
Posts: 3
Default

Compiled and cufflinks test passed!

After getting updated gcc onto a private folder of the cluster I installed boost

Code:
cd boost_1_55_0b1
echo "using gcc : 4.8.2 : $scr/bin/g++ ; " >> tools/build/v2/user-config.jam
./bootstrap.sh --prefix=$scr --with-toolset=gcc
./bjam --prefix=$scr link=static \
 runtime-link=static stage install
and cufflinks using the new gcc and adding rt to the LIBS to correct another error relate to "time":

Code:
cd cufflinks-2.1.1
CC=$scr/bin/gcc CXX=$scr/bin/g++ ./configure --prefix=$scr --with-boost=$scr --with-boost-libdir=$scr/lib --with-eigen=$scr/include --with-bam=$scr
echo "LIBS = -lz -lrt" >> $scr/installation_files/cufflinks-2.1.1/src/Makefile
make
make install
Additionally I always have to export the LD_LIBRADY_PATH for the new lib before running cufflinks or tophat with the updated gcc.

Code:
export LD_LIBRARY_PATH=$scr/lib:$LD_LIBRARY_PATH
both tophat and cufflinks were able to analyse their respective testdata.

Thanks a lot guys!!
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boost, cufflinks, cufflinks 2.1.1, next_bundle_ref_driven, posix_category

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